US10246696B2 - Pectinases with improved thermostability - Google Patents

Pectinases with improved thermostability Download PDF

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US10246696B2
US10246696B2 US16/062,595 US201616062595A US10246696B2 US 10246696 B2 US10246696 B2 US 10246696B2 US 201616062595 A US201616062595 A US 201616062595A US 10246696 B2 US10246696 B2 US 10246696B2
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Klara Birikh
Anu Minna Maaret Suonpaa
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Metgen Oy
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/88—Lyases (4.)
    • C—CHEMISTRY; METALLURGY
    • C11—ANIMAL OR VEGETABLE OILS, FATS, FATTY SUBSTANCES OR WAXES; FATTY ACIDS THEREFROM; DETERGENTS; CANDLES
    • C11D—DETERGENT COMPOSITIONS; USE OF SINGLE SUBSTANCES AS DETERGENTS; SOAP OR SOAP-MAKING; RESIN SOAPS; RECOVERY OF GLYCEROL
    • C11D3/00—Other compounding ingredients of detergent compositions covered in group C11D1/00
    • C11D3/16—Organic compounds
    • C11D3/38—Products with no well-defined composition, e.g. natural products
    • C11D3/386—Preparations containing enzymes, e.g. protease or amylase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/70—Vectors or expression systems specially adapted for E. coli
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y402/00—Carbon-oxygen lyases (4.2)
    • C12Y402/02—Carbon-oxygen lyases (4.2) acting on polysaccharides (4.2.2)
    • C12Y402/02002—Pectate lyase (4.2.2.2)

Definitions

  • the invention is in the field of protein chemistry, in particular in the field of enzymology. It provides pectinases, i.e. polypeptides with pectin-degrading properties. In particular the invention provides polypeptides with pectate lyase activity (EC 4.2.2.2). Enzymes according to the invention have improved properties, such as improved thermostability.
  • Plant cell wall degrading enzymes are carbohydrate-active enzymes that have been classified in different families based on homology criteria [http://www.cazy.org/, Cantarel et al., 2009, Nucleic Acids Res 37: D233-D238].
  • Pectate lyases (EC 4.2.2.2), are an important group of plant cell wall degrading enzymes. They cleave pectin using an eliminative cleavage of (1 ⁇ 4)-alpha-D-galacturonan yielding oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends. They are mainly produced by plant pathogens and plant-associated organisms, and only rarely by animals. Pectate lyases are also commonly produced in bacteria, either by bacteria living in close proximity with plants or by gut bacteria that find plant material in the digestive tract of their hosts. [Hugoucreme-Cotte-Pattat et al., Environmental Microbiology reports (2014) doi 10, 1111/1758-2229, 12166].
  • Pectate lyases favor pectate, the anion, over pectin, the methylated ester, which is the preferred substrate of pectin lyase EC 4.2.2.10.
  • Pectate lyases are also known under different names, such as alpha-1,4-D-endopolygalacturonic acid lyase, endo-alpha-1,4-polygalacturonic acid lyase, endogalacturonate transeliminase, endopectin methyltranseliminase, pectate transeliminase, pectic acid lyase, pectic acid transeliminase, pectic lyase, pectin trans-eliminase, PGA lyase, polygalacturonate lyase, polygalacturonic acid lyase, polygalacturonic acid trans-eliminase, polygalacturonic transelimin
  • pectate lyases When pectate lyases are used in industrial processes, it is often advantageous that they are stable at higher temperatures (thermostable) and resistant to alkaline conditions. Thermostable alkaline pectate lyases for instance have potential applications in the textile industry as an alternative to chemical-based ramie degumming processes. Such enzymes have been described, and have been isolated and characterized from bacterial sources, mainly Bacillus [Swarupa Rani chiliveri et al., Carbohydrate Polymers (2014), 111: 264-272, Zhou et al., Appl Environ Microbiol (2015) 81: 5714-5723].
  • Cleavage by pectate lyases requires the presence of cations, such as manganese, nickel, iron, cobalt or calcium ions [Celia Marin-Rodriguez et al., J. Exp. Bot. (2002) 53: 2115-2119, Hugouuben-Cotte-Pattat et al., Environmental Microbiology reports (2014) doi 10, 1111/1758-2229, 12166], with only rare exceptions [Kazemi-Pour et al., Proteomics (2004) 10: 3177-3186].
  • cations such as manganese, nickel, iron, cobalt or calcium ions
  • thermostable pectate lyase was isolated from Bacillus , cloned, sequenced and characterized [Takao et al, Biosci. Biotechnol. Biochem. (2000) 64: 2360-2367, Takao et al., Biosci. Biotechnol. Biochem. (2001) 65: 322-329].
  • thermostable enzyme was described to be thermostable when produced in a homologous expression system in Bacillus subtilis , and capable of resisting pre-incubation for 30 minutes at 70 degrees Celsius [Takao et al., Biosci. Biotechnol. Biochem. (2001) 65: 322-329]. However, pre-incubation at 80 degrees Celsius completely abolished the enzymatic activity. Because many industrial processes are preferably performed at temperatures above 70 degrees Celsius, there is a need in the art for even more thermostable or thermoresistant polypeptides with pectate lyase activity.
  • the present invention addresses this need in that it provides a pectate lyase with improved thermostable properties. More in particular, the invention provides a polypeptide with pectate lyase activity comprising an amino acid sequence that is at least 70% identical to the amino acid according to SEQ ID NO: 1, wherein the polypeptide comprises a small, polar, non-charged amino acid residue at an amino acid position corresponding to position 235 in SEQ ID NO: 1.
  • the invention also relates to a composition comprising a polypeptide as described above, a nucleic acid encoding a polypeptide as described above, a vector comprising such a nucleic acid and a composition comprising such a nucleic acid or a vector.
  • the invention also provides a recombinant host cell comprising a nucleic acid, a vector or a composition as described above.
  • the invention relates to a method for producing a polypeptide as described above, comprising the steps of: culturing a recombinant host cell as described above, under conditions suitable for the production of the polypeptide, and recovering the polypeptide obtained, and optionally purifying the polypeptide.
  • the invention relates to a polypeptide as described above in an application selected from the group consisting of pulp delignification, degrading or decreasing the structural integrity of lignocellulosic material, textile dye bleaching, wastewater detoxifixation, xenobiotic detoxification, production of a sugar from a lignocellulosic material and recovering cellulose from a biomass.
  • the invention also relates to a method for improving the thermostability of a polypeptide with pectate lyase activity comprising an amino acid sequence that is at least 70% identical to the amino acid according to SEQ ID NO: 1, the method comprising the step of altering the amino acid at a position corresponding to position 235 in SEQ ID NO: 1 to a a small, polar, non-charged amino acid residue.
  • FIG. 1 Diagram showing the relative pectate lyase activity of polypeptides according to SEQ ID NO: 1 (WT) and its K235 variants SEQ ID NO: 2 (K235T), SEQ ID NO: 3 (K235S), SEQ ID NO: 4 (K235N), and SEQ ID NO: 5 (K235C).
  • Pectate lyase activity was determined after a pre-incubation of 10 minutes at elevated temperatures.
  • RT Room Temperature, 70 C is 70 degrees Celsius.
  • FIG. 2 Diagram showing the relative pectate lyase activity of polypeptides according to SEQ ID NO: 6 (93% identity with SEQ ID NO: 1), and its K235 variants SEQ ID NO: 7 (K235T), SEQ ID NO: 8 (K235S), SEQ ID NO: 9 (K235N), and SEQ ID NO: 10 (K235C).
  • Pectate lyase activity was determined after a pre-incubation of 10 minutes at elevated temperatures.
  • RT Room Temperature, 70 C is 70 degrees Celsius.
  • FIG. 3 Diagram showing the relative pectate lyase activity of polypeptides according to SEQ ID NO: 11 (89% identity with SEQ ID NO: 1), and its K235 variants SEQ ID NO: 12 (K235T), SEQ ID NO: 13 (K235S), SEQ ID NO: 14 (K235N), and SEQ ID NO: 15 (K235C).
  • Pectate lyase activity was determined after a pre-incubation of 10 minutes at elevated temperatures.
  • RT Room Temperature, 70 C is 70 degrees Celsius.
  • FIG. 4 Diagram showing the relative pectate lyase activity of polypeptides according to SEQ ID NO: 1 (WT) and its variants A231L, K235S, K235T, A231L+K235S and A231L+K235T.
  • Pectate lyase activity was determined after a pre-incubation of 10 minutes at elevated temperatures.
  • RT Room Temperature, 70 C is 70 degrees Celsius.
  • the present invention is based on our observation that a single amino acid substitution (K235 variant) in different pectate lyases improves their thermostability.
  • amino acid substitution is used herein the same way as it is commonly used, i.e. the term refers to a replacement of one or more amino acids in a protein with one or more other amino acids. Such an amino acid substitution may also be referred to as a mutation, a variation or a variant.
  • the invention thus relates to a polypeptide with pectate lyase activity comprising an amino acid sequence that is at least 70% identical to the amino acid according to SEQ ID NO: 1, wherein the polypeptide comprises a small, polar, non-charged amino acid residue at an amino acid position corresponding to position 235 in SEQ ID NO: 1.
  • Polypeptides with pectate lyase activity are also referred herein as pectate lyases, or pectate lyase enzymes.
  • pectate lyase activity is used herein to indicate the ability of a polypeptide to cleave pectin using an eliminative cleavage of (1 ⁇ 4)-alpha-D-galacturonan yielding oligosaccharides with 4-deoxy-alpha-D-galact-4-enuronosyl groups at their non-reducing ends.
  • the term “at least 70%” is used herein to include at least 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 82%, 83%,%, 85%, 88%, 87%, 88%, 89%, 90% or more, such as 91%, 92%, 93%, 94%, 95%, 99%, 97%, 98%, 99%, or even 100%.
  • the alignment of two sequences is to be performed over the full length of the polypeptides.
  • the comparison (aligning) of sequences is a routine task for the skilled person and can be accomplished using standard methods known in the art.
  • Other commercial and open software such as Vector NTI are also suitable for this purpose,
  • SEQ ID NO: 1 provides the amino acid sequence of a known polypeptide [Takao et al, Biosci. Biotechnol. Biochem. (2000) 64: 2360-2367, Takao et al., Biosci. Biotechnol. Biochem. (2001) 65: 322-329] with pectate lyase activity.
  • Exemplified herein are the variants K235T, K235C, K235S and K235N.
  • mutant protein or “mutation” is also used herein to refer to a polypeptide with pectate lyase activity as described herein, wherein the polypeptide comprises a small, polar, non-charged amino acid residue at an amino acid position corresponding to position 235 in SEQ ID NO: 1.
  • wild type protein is also used herein to indicate a polypeptide identical to the mutant protein, with the exception that it does not comprise a small, polar, non-charged amino acid residue at an amino acid position corresponding to position 235 in SEQ ID NO: 1.
  • thermostability in reference to a mutant polypeptide, as used herein, means that the mutant polypeptide has a higher residual pectate lyase activity than the corresponding wild type protein, after incubation for 10 minutes in 50 mM Tris-HCl pH 8.0 at a suitable temperature.
  • suitable temperature refers to a temperature at which the wild type protein loses part of its pectate lyase activity after 10 minutes of incubation in 50 mM Tris-HCl pH 8.0.
  • suitable temperature refers to a temperature chosen from a temperature range between temperatures X and Y, wherein X is the lowest temperature at which a wild type polypeptide shows a detectable loss of activity after 10 minutes of incubation in 50 mM Tris-HCl pH 8.0 and wherein temperature Y is the lowest temperature at which a wild type polypeptide loses all activity after 10 minutes of incubation in 50 mM Tris-HCl pH 8.0.
  • thermostability assay the polypeptides were heated to 70, 75 or 80 degrees Celsius for 10 minutes in 50 mM Tris-HCl at pH 8.0.
  • the residual activity was measured at 60 degrees Celsius at pH 8.0 as described in example 5 and compared to the residual activity of the same polypeptides after preincubation at room temperature for 10 minutes. The results are shown in FIGS. 1-3 .
  • the wild type sequence (SEQ ID NO: 1) only displayed 60% of its activity when pre-incubated at 70 degrees Celsius for 10 minutes
  • the variant polypeptides with the 235 mutation (K235T, K235S, K235N and K235C) were all at least as active as when pre-incubated at room temperature (table 1 and FIG. 1 ).
  • the wild-type enzyme (WT, SEQ ID NO: 1) was not active anymore after pre-incubation at 75 degrees Celsius for 10 minutes
  • the K235 variants where active, even up to a level of 50% of the activity of the same enzyme, pre-incubated at room temperature for 10 minutes ( FIG. 1 ).
  • the amino acid corresponding to position 235 in SEQ ID NO: 1 is to be understood as follows. If such a position is to be determined in a given amino acid sequence that is at least 70% identical with the amino acid sequence according to SEQ ID NO: 1, then the two sequences are first to be aligned. That may be done by routine methods and software available in the art. The amino acid in the given amino acid sequence corresponding to amino acid 235 in SEQ ID NO: 1 is then the amino acid aligning with the lysine residue at position 235 in SEQ ID NO: 1.
  • amino acid variant has a meaning well recognized in the art and is accordingly used herein to indicate an amino acid sequence that has at least one amino acid difference as compared to another amino acid sequence, such as the amino acid sequence from which it was derived.
  • homologous polypeptides having 93% and 89% sequence identity to the wild type sequence according to SEQ ID NO: 1. These homologous polypeptides are referred to herein as polypeptides according to SEQ ID NO: 6 (93% identical) and SEQ ID NO: 11 (89% identical).
  • K235 variants of these polypeptides also had an improved thermostability (tables 2 and 3 and FIGS. 2 and 3 ).
  • thermostability means that the K235 variant polypeptides exhibited more pectate lysase activity after preincubation at elevated temperatures as compared to the activity of the same polypeptides without the mutation at position 235, such as the wild type sequence (SEQ ID NO: 1) or the two homologous polypeptides according to SEQ ID NO: 6 and SEQ ID NO: 11 as described herein.
  • Thermostable pectate lyases have been described to be produced by bacteria of the genus Bacillus [Takao et al, Biosci. Biotechnol. Biochem. (2000) 64: 2360-2367, Takao et al., Biosci. Biotechnol. Biochem.
  • the invention relates to a polypeptide as described herein wherein the polypeptide is capable of being expressed in a bacterium, such as a Bacillus species, more preferably Bacillus subtilis.
  • polypeptides may be produced that are homologous to the wild-type sequence and still retain their pectate lyase activity.
  • a BLAST search revealed that pectate lyases are available from bacterial origin, in particular from Bacillus species, with an identity as low as 52% or less as compared to SEQ ID NO: 1.
  • the skilled person will therefore have no difficulty in constructing a polypeptide with pectate lyase activity that is at least 70% identical to the sequence of SEQ ID NO: 1 following the procedures and guidance provided herein. He will also be able to make the K235 variants as described herein, thereby obtaining a pectate lyase with an improved thermostability.
  • the invention relates to a polypeptide as described herein comprising an amino acid sequence that is at least 75% identical to the amino acid according to SEQ ID NO: 1, such as 80%, 85%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or even 100%.
  • Recovery of a polypeptide according to the invention as produced by a host cell may be performed by any technique known to those skilled in the art. Possible techniques include, but are not limited to secretion of the protein into the expression medium, and purification of the protein from cellular biomass.
  • the production method may further comprise a step of purifying the polypeptide obtained.
  • thermostable polypeptides non-limiting examples of such methods include heating of the disintegrated cells and removing coagulated thermo labile proteins from the solution.
  • secreted proteins non-limiting examples of such methods include ion exchange chromatography, and ultra-filtration of the expression medium. It is preferred that the purification method of choice is such that the purified protein retains its activity.
  • the invention relates to a polypeptide as described herein wherein the polypeptide is an isolated polypeptide.
  • polypeptides as described herein may be used in compositions containing several additional components, such as stabilizers, fillers, cell debris, culture medium etcetera.
  • additional components such as stabilizers, fillers, cell debris, culture medium etcetera.
  • the invention provides a composition comprising a polypeptide as described herein.
  • heterologous expression system or equivalent means a system for expressing a DNA sequence from one host organism in a recipient organism from a different species or genus than the host organism.
  • the most prevalent recipients known as heterologous expression systems, are chosen usually because they are easy to transfer DNA into or because they allow for a simpler assessment of the protein's function.
  • Heterologous expression systems are also preferably used because they allow the upscaling of the production of a protein encoded by the DNA sequence in an industrial process.
  • Preferred recipient organisms for use as heterologous expression systems include bacterial, fungal and yeast organisms, such as for example Escherichia coli, Bacillus, Corynebacterium, Pseudomonas, Pichia pastoris, Saccharomyces cerevisiae, Yarrowia lipolytica , filamentous fungi and many more systems well known in the art.
  • polypeptides or proteins may be fused to additional sequences, by attaching or inserting, including, but not limited to, affinity tags, facilitating protein purification (S-tag, maltose binding domain, chitin binding domain), domains or sequences assisting folding (such as thioredoxin domain, SUMO protein), sequences affecting protein localization (periplasmic localization signals etc), proteins bearing additional function, such as green fluorescent protein (GFP), or sequences representing another enzymatic activity.
  • affinity tags facilitating protein purification (S-tag, maltose binding domain, chitin binding domain
  • domains or sequences assisting folding such as thioredoxin domain, SUMO protein
  • sequences affecting protein localization periplasmic localization signals etc
  • proteins bearing additional function such as green fluorescent protein (GFP)
  • GFP green fluorescent protein
  • Other suitable fusion partners for the presently disclosed polypeptides are known to those skilled in the art.
  • the present invention also relates to polynucleotides encoding any of the pectate lyase variants disclosed herein. Means and methods for cloning and isolating such polynucleotides are well known in the art.
  • control sequences are readily available in the art and include, but are not limited to, promoter, leader, polyadenylation, and signal sequences.
  • Pectate lyase variants may be obtained by standard recombinant methods known in the art. Briefly, such a method may comprise the steps of: culturing a recombinant host cell as described above under conditions suitable for the production of the polypeptide, and recovering the polypeptide obtained. The polypeptide may then optionally be further purified.
  • vectors include, but are not limited to, plasmids or modified viruses which are maintained in the host cell as autonomous DNA molecule or integrated in genomic DNA.
  • the vector system must be compatible with the host cell used as is well known in the art.
  • suitable host cells include bacteria (e.g. E. coli , bacilli), yeast (e.g. Pichia Pastoris, Saccharomyces Cerevisiae ), fungi (e.g. filamentous fungi) insect cells (e.g. Sf9).
  • the invention relates to a method for improving the thermostability of a polypeptide with pectate lyase activity comprising an amino acid sequence that is at least 70% identical to the amino acid according to SEQ ID NO: 1, the method comprising the step of altering the amino acid at a position corresponding to position 235 in SEQ ID NO: 1 to a small, polar, non-charged amino acid residue.
  • thermostability of the above described K235 variant polypeptides could be even further improved if another variation was introduced in addition to the K235 variation.
  • A231L variant indicates that the amino acid corresponding to the residue at position 231 of SEQ ID NO: 1 (alanine) is replaced by a leucine residue.
  • the polypeptides carrying both the A231L variation and the K235 variations were more thermostable than each of the variant polypeptides alone.
  • the effect was even found to be synergistic.
  • the polypeptide according to SEQ ID NO: 1 did not have any significant residual activity after pre-incubation at 75 degrees C.
  • the A231L variant as well as the K235T and K235S variants retained 20%, 50% and 50% of their activity relative to the activity after pre-incubation at room temperature (relative activity, table 4 and FIG. 4 ).
  • the relative activity of this double mutant after pre-incubation at 75 C
  • the same effect was found for the A231L and K235S double mutant of the polypeptide according to SEQ ID NO: 1.
  • the activity of the double mutant remained at 100% after pre-incubation at 75 degrees Celsius for 10 minutes.
  • the double mutants were exceptionally active after pre-incubation at 80 degrees Celsius.
  • the A231L variant of SEQ ID NO: 1 was no longer active after pre-incubation at 80 degrees Celsius, in combination with the K235 variants, it improved the thermostability from K235T variant from 35% to 80% and the thermostability of the K235S variant from 35 to 70% (table 4, FIG. 4 )
  • thermostability of these polypeptides could also be improved in the same manner as described above for the polypeptide according to SEQ D NO: 1.
  • the single mutation A231L in SEQ ID NO: 6 improved the thermostability as shown in table 5.
  • the double mutant A231L plus K235N improved the thermostability synergistically, i.e. more than the sum of the contributions of each of the mutations separately.
  • the relative activity of the A231L and K235N variants still was 25% and 30% respectively, whereas the combination of both mutations resulted in 80% relative activity.
  • the double mutants were exceptionally active after pre-incubation at 80 degrees Celsius.
  • the A231L variant of SEQ ID NO: 1 was not significantly active after pre-incubation at 80 degrees Celsius.
  • it improved the thermostability of the double mutant from 20% to 70% (table 5, FIG. 5 ).
  • the single mutation A231L in SEQ ID NO: 11 improved the thermostability as shown in table 6.
  • the double mutant A231L plus K235C improved the thermostability synergistically, i.e. more than the sum of the contributions of each of the mutations separately.
  • the A231L and K235C variants still had 18% and 35% relative activity respectively, whereas the combination of both mutations resulted in 90% relative activity.
  • the double mutants were exceptionally active after pre-incubation at 80 degrees Celsius.
  • the A231L variant of SEQ ID NO: 11 was not significantly active after pre-incubation at 80 degrees Celsius.
  • it improved the thermostability of the double mutant from 10% to 80% (table 6, FIG. 6 ).
  • the invention also relates to a K235 variant polypeptide as described above additionally comprising a leucine residue at an amino acid position corresponding to position 231 in SEQ ID NO: 1.
  • the invention also relates to a method for improving the thermostability of a polypeptide with pectate lyase activity comprising an amino acid sequence that is at least 70% identical to the amino acid according to SEQ ID NO: 1, the method comprising the step of altering the amino acid at a position corresponding to position 235 in SEQ ID NO: 1 to a small, polar, non-charged amino acid residue and altering the amino acid at a position corresponding to position 231 in SEQ ID NO: 1 to a leucine residue.
  • the invention relates to any of the methods as described above, wherein the polypeptide with pectate lyase activity is capable of being expressed in a bacterium, such as a Bacillus species, more preferably Bacillus subtilis.
  • polypeptides with pectate lyase activity may be used in a wide range of different industrial processes and applications, such as cellulose recovery from lignocellulosic biomass, decreasing the energy required for the refining of wood and production of a sugar from a lignocellulosic material. They may also be used in wood pulp preparation, in pulp delignification, textile dye bleaching, wastewater detoxifixation, xenobiotic detoxification, degrading or decreasing the structural integrity of lignocellulosic material and detergent manufacturing.
  • Example 1 Preparation of a Polypeptide According to SEQ ID NO: 1
  • the DNA construct disclosed in Takao et al., Biosci. Biotechnol. Biochem. (2001) 65: 322-329 encoding the polypeptide according to SEQ ID NO: 1 was optimized for expression in E. coli and commercially synthesized and cloned into a standard plasmid vector pET28a+ under the control of T7-RNA-polymerase promoter for expression in Escherichia coli BL21(DE3).
  • the nucleotide sequence of the construct is provided herein as SEQ ID NO: 16.
  • Example 2 Preparation of Variants of a Polypeptide According to SEQ ID NO: 1 with Pectate Lyase Activity
  • Homologous protein sequences (according to SEQ ID NO: 6 and SEQ ID NO: 11) were generated by random mutagenesis of SEQ ID NO:s 16 and SEQ ID NO: 21 using error-prone PCR essentially as described (Curr Protoc Mol Biol. 2001 May; Chapter 8: Unit 8.3. doi: 10.1002/0471142727.mb0803s51, Random mutagenesis by PCR. Wilson DS1, Keefe AD) using a commercial random PCR mutagenesis kit (QuikChange® II XL Site-Directed Mutagenesis kit by Agilent Technologies). More in particular, the DNA sequence of SEQ ID NO: 21 was obtained from SEQ ID NO: 16 encoding the polypeptide according to SEQ ID NO: 1.
  • SEQ ID NO: 26 was obtained by random mutagenesis of SEQ ID NO: 21 encoding the polypeptide according to SEQ ID NO: 6.
  • SEQ ID NO: 26 is the DNA sequence encoding the polypeptide according to SEQ ID NO: 11.
  • PCR fragments resulting from error-prone PCR were cloned to the plasmid vector pET28a+ under the control of T7-RNA-polymerase promoter for expression in Escherichia coli BL21 (DE3), and screened for pectate lyase activity of the recombinant proteins.
  • the polypeptide according to SEQ ID NO: 6 exhibited pectate lyase activity and was found to be 93% identical with SEQ ID NO: 1.
  • the polypeptide according to SEQ ID NO: 11 also exhibited pectate lyase activity and was found to be 89% identical with SEQ ID NO: 1.
  • polypeptide according to SEQ ID NO:s 2-5 mutations were inserted into the DNA coding for polypeptide according to SEQ ID NO: 1 at position 235.
  • the lysine residue from that position in SEQ ID NO: 1 was replaced with either one of the residues T (threonine), C (cysteine), S (serine) or N (asparagine), thereby resulting in the polypeptides according to SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4 and SEQ ID NO: 5, respectively.
  • K235T K235S
  • K235N K235C
  • recombinant gene without the mutation was used as the template.
  • Primers 1 and 4 bind inside the vector sequence and are not specific to the recombinant gene.
  • Primers 2 and 3 bind inside the recombinant gene and their binding sites overlap.
  • Primer 3 binding site contains the mutation site.
  • Primer 3 represents the mutated (desired) sequence, which is not 100% matching the template (lower case type font in the primer sequence indicates the mismatched nucleotides). However, the primer has enough affinity and specificity to the binding site to produce the desired PCR product.
  • Purified PCR products from reactions (1) and (2) were combined and used as template for PCR reaction with Primer 1 and Primer 4. The products of this reaction, containing the A231L variant sequence of the genes encoding the polypeptides according to SEQ ID NO:s 48-50 was cloned in a plasmid vector for expression in E. coli.
  • Double mutants were prepared by introducing the mutation into the DNA encoding a polypeptide carrying a single mutation.
  • recombinant genes were cloned into pET-28 commercial expression vector under the control of T7 bacteriophage promoter.
  • Protein production was carried out in E. coli BL21(DE3) strain according to the plasmid manufacturer protocol available at http://richsingiser.com/4402/Novagen%20pET%20system%20manual.pdf.
  • the incubation temperature for protein production was 30 degrees C., which was found optimal for maximum yield of the active protein.
  • Cells were lysed using lysis buffer (50 mM Tris-HCl pH7.4, 1% Triton X100, 0.5 mM CaCl) and heated at 60 degrees C. for 20 min. Coagulated cell debris was removed by centrifugation.
  • the thermostable recombinant pectate lyases were detected in the soluble fraction only, consistent with the notion that they were thermostable enzymes.
  • Pectate lyase activity assay was carried out essentially as described in Takao M, Nakaniwa T, Yoshikawa K, Terashita T, Sakai T., “Purification and characterization of thermostable pectate lyase with protopectinase activity from thermophilic Bacillus sp. TS 47”. Biosci Biotechnol Biochem. 2000 64:2360-7.
  • pectate lyase activity was assayed by measuring the increase in absorbance at 235 nm of the reaction mixture.
  • Polygalacturonic acid (PGA) sodium salt from de-methylated citrus pectin purchased from MegaZyme
  • a reaction mixture containing 1 ml of 0.1% PGA in 10 mM Tris-HCl buffer, pH 8.0 and 0.5 mM CaCl2, and an appropriate amount of enzyme solution was incubated for 30 min at 60 C.
  • reaction was stopped by placing the mixture in 100 degrees C. (boiling water bath) for 5 min.
  • Relative pectate lyase activity was was calculated from the difference in absorption of the reaction mixture at 235 nm at the start and at the end of the reaction.
  • Thermostability of the polypeptides with pectate lyase activity was determined by pre-incubation for 10 minutes in 50 mM Tris-HCl pH 8.0, either at room temperature (control) or at 70 degrees C., 75 degrees C. and 80 degrees C. before measuring their activity according to example 5.
  • Amino acid sequence and nucleotide sequences are provided herewith in the WIPO ST_25 standard. For convenience the sequences are also provided in table 8.
  • SEQ ID NO: 1 is derived from the prior art and has been disclosed in Takao et al, Biosci. Biotechnol. Biochem. (2000) 64: 2360-2367 and in Takao et al., Biosci. Biotechnol. Biochem. (2001) 65: 322-329.
  • Amino acids corresponding to positions 231 and 235 in SEQ ID NO: 1 are shown in bold and underlined type face.
  • SEQ ID NO: 6 was obtained by random mutagenesis of the DNA encoding SEQ ID NO: 1 (shown herein as SEQ ID NO: 16) as described in example 2.
  • SEQ ID NO: 11 was obtained by random mutagenesis of the DNA encoding SEQ ID NO: 6 (shown herein as SEQ ID NO: 21).
  • SEQ ID NO: 26 The DNA encoding the polypeptide according to SEQ ID NO: 11 is shown herein as SEQ ID NO: 26.
  • amino acids deviating from the wild type sequence of SEQ ID NO: 1 are shown in capital letters.
  • polypeptide according to SEQ ID NO: 6 is a homologue of the polypeptide according to SEQ ID NO: 1. These two polypeptides have 385 of the 416 amino acids in common, in other words they are 93% identical.
  • polypeptide according to SEQ ID NO: 11 is also a homologue of the polypeptide according to SEQ ID NO: 1. These two polypeptides have 369 of the 416 amino acids in common, in other words they are 89% identical.
  • polypeptides according to SEQ ID NO:s 2-5 correspond to the polypeptide according to SEQ ID NO: 1 with variations K235T, K235S, K235N and K235C respectively.
  • polypeptides according to SEQ ID NO:s 7-10 correspond to the polypeptide according to SEQ ID NO: 6 with variations K235T, K235S. K235N and K235C respectively.
  • polypeptides according to SEQ ID NO:s 12-15 correspond to the polypeptide according to SEQ ID NO: 11 with variations K235T, K235S, K235N and K235C respectively.
  • nucleotide sequences according to SEQ ID NO:s 16-30 encode the polypeptides with amino acid sequences according to SEQ ID NO:s 1-15 respectively.
  • SEQ ID NO:s 31-39 correspond to the primers used for producing the variant polypeptides as detailed in example 3.
  • Polypeptides carrying the double mutations A231L with K235T, K235S, K235N and K235C double mutations are shown in SEQ ID NO: 40-43 respectively.
  • DNA encoding the polypeptides according to SEQ ID NO: 40-43 are shown in SEQ ID NO: 44-47.
  • SEQ ID NO:s 48, 49 and 50 correspond to variants A231L in polypeptides according to SEQ ID NO: 1, 6 and 11 respectively.
  • SEQ ID NO:s 51-53 are the DNA sequences encoding the polypeptides according to SEQ ID NO:s 48-50

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Chiliveri et al., A Novel Thermostable, Alkaline Pectate Lyase from Bacillus Tequilensis SV11 with Potential in Textile Industry, Elsevier, Nov. 10, 2013, pp. 264-272.
Database UniProt [Online], "SubName: Full=Ptate lyase {ECO:0000313|EMBL:KIL52125.1}; EC=4.2.2.2 {ECO:0000313|EMBL:KIL52125.1};" retrieved from EBI accession No. UNIPROT:A0A0C2RPE1, Apr. 1, 2015, 2 pgs.
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Liang et al., Improving the Thermoactivity and Thermostability of Pectate Lyase from Bacillus Pumilus for Ramie Degumming, Appl Microbiol Biotechnol, Jul. 12, 2014, pp. 2673-2682.
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Xiao et al., Improvement of the Thermostability and Activity of a Pectate Lyase by Single Amino Acid Substitutions, Using a Strategy Based on Melting-Temperature-guided Sequence Alignment, Applied and Environmental Microbiology, Feb. 2008, pp. 1183-1189, vol. 74 No. 4.

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US11008562B2 (en) * 2015-12-15 2021-05-18 Metgen Oy Calcium independent pectinases with improved thermostability

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